I quite regularly patch files between a windows and mac system and patch does seem to deal with the newlines correctly so I don't think that's the issue. It looks like may you've deleted test_licstatactioncontainers.cpp and the first warning is about that. The second appears to be complaining about not finding the file itself.

Could this be a filename case issue? Windows is insensitive to filename case, but linux isn't. Is the file actually called Test_LicenceServerUsageMap.cpp on linux perchance? Or the directory LicStat/Test ?